Align ATPase (characterized, see rationale)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__PS:Dsui_2068 Length = 278 Score = 153 bits (386), Expect = 4e-42 Identities = 91/209 (43%), Positives = 127/209 (60%), Gaps = 10/209 (4%) Query: 43 LTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL-SHDRRDIATIRQEVG 101 L V GE+ ++G SG+GKST LR N LE G++ + G L + D+ T RQ +G Sbjct: 35 LDVAPGEIHGIIGFSGAGKSTLLRLANLLERPDAGQVVVHGQDLMTLSPADLRTARQRIG 94 Query: 102 MVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGG 161 M+FQ FNL + TV N+ P+++ A+ + LE V ++E+A YP QLSGG Sbjct: 95 MIFQHFNLLHNRTVADNVAF-PLRIAGADEARINERVKTCLEFVGLSEKAGVYPAQLSGG 153 Query: 162 QQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASE-GMTMLVATHEVGFA 220 Q+QRVAIARALA +P +LL DEPTSALDP + +L+V+ D+ G+T+L+ +HE+G Sbjct: 154 QKQRVAIARALAPEPHVLLADEPTSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGVI 213 Query: 221 REVADRVVLMADGQIVE-------EAPPD 242 R + RV +M GQIVE PPD Sbjct: 214 RRLCHRVSVMEAGQIVERLTIANGRIPPD 242 Lambda K H 0.321 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 214 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 261 Length of database: 278 Length adjustment: 25 Effective length of query: 236 Effective length of database: 253 Effective search space: 59708 Effective search space used: 59708 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory